forked from lijiext/lammps
135 lines
3.7 KiB
C++
135 lines
3.7 KiB
C++
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
http://lammps.sandia.gov, Sandia National Laboratories
|
|
Steve Plimpton, sjplimp@sandia.gov
|
|
|
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
certain rights in this software. This software is distributed under
|
|
the GNU General Public License.
|
|
|
|
See the README file in the top-level LAMMPS directory.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
|
|
Paul Crozier (SNL)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "math.h"
|
|
#include "stdlib.h"
|
|
#include "string.h"
|
|
#include "fix_spring_rg.h"
|
|
#include "atom.h"
|
|
#include "update.h"
|
|
#include "group.h"
|
|
#include "respa.h"
|
|
#include "domain.h"
|
|
#include "error.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace FixConst;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) :
|
|
Fix(lmp, narg, arg)
|
|
{
|
|
if (narg != 5) error->all(FLERR,"Illegal fix spring/rg command");
|
|
|
|
k = atof(arg[3]);
|
|
rg0_flag = 0;
|
|
if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1;
|
|
else rg0 = atof(arg[4]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int FixSpringRG::setmask()
|
|
{
|
|
int mask = 0;
|
|
mask |= POST_FORCE;
|
|
mask |= POST_FORCE_RESPA;
|
|
return mask;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixSpringRG::init()
|
|
{
|
|
masstotal = group->mass(igroup);
|
|
|
|
// if rg0 was specified as NULL, compute current Rg
|
|
// only occurs on 1st run
|
|
|
|
if (rg0_flag) {
|
|
double xcm[3];
|
|
group->xcm(igroup,masstotal,xcm);
|
|
rg0 = group->gyration(igroup,masstotal,xcm);
|
|
rg0_flag = 0;
|
|
}
|
|
|
|
if (strstr(update->integrate_style,"respa"))
|
|
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixSpringRG::setup(int vflag)
|
|
{
|
|
if (strstr(update->integrate_style,"verlet"))
|
|
post_force(vflag);
|
|
else {
|
|
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
|
|
post_force_respa(vflag,nlevels_respa-1,0);
|
|
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixSpringRG::post_force(int vflag)
|
|
{
|
|
// compute current Rg and center-of-mass
|
|
|
|
double xcm[3];
|
|
group->xcm(igroup,masstotal,xcm);
|
|
double rg = group->gyration(igroup,masstotal,xcm);
|
|
|
|
// apply restoring force to atoms in group
|
|
// f = -k*(r-r0)*mass/masstotal
|
|
|
|
double dx,dy,dz,term1;
|
|
|
|
double **f = atom->f;
|
|
double **x = atom->x;
|
|
int *mask = atom->mask;
|
|
int *type = atom->type;
|
|
tagint *image = atom->image;
|
|
double *mass = atom->mass;
|
|
int nlocal = atom->nlocal;
|
|
|
|
double massfrac;
|
|
double unwrap[3];
|
|
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit) {
|
|
domain->unmap(x[i],image[i],unwrap);
|
|
dx = unwrap[0] - xcm[0];
|
|
dy = unwrap[1] - xcm[1];
|
|
dz = unwrap[2] - xcm[2];
|
|
term1 = 2.0 * k * (1.0 - rg0/rg);
|
|
massfrac = mass[type[i]]/masstotal;
|
|
f[i][0] -= term1*dx*massfrac;
|
|
f[i][1] -= term1*dy*massfrac;
|
|
f[i][2] -= term1*dz*massfrac;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop)
|
|
{
|
|
if (ilevel == nlevels_respa-1) post_force(vflag);
|
|
}
|